The reason it's not updating properly is because you've
committed your .yardoc directory, which you should not be doing.
It's causing the updates to fail (this directory is machine
generated). Remove that from your repo and gitignore it, and
updating should start to work.

"On two occasions I have been asked [by members of Parliament], 'Pray,
Mr. Babbage, if you put into the machine wrong figures, will the right
answers come out?' I am not able rightly to apprehend the kind of
confusion of ideas that could provoke such a question."